Research workbench
Structural basis of tubulin recruitment and assembly by microtubule polymerases with tumor overexpressed gene (tog) domain arrays
Analyse Structural basis of tubulin recruitment and assembly by microtubule polymerases… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MZF
- Type
- protein
- Length
- 9,989 residues
- Chains
- 28
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tubulin alpha-1A chain; Tubulin beta chain; Protein STU2P/ALP14P; Designed ankyrin repeat…
- UniProt
- P02550, P02554
- Ligands
- GTP, GDP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 7 distinct chains · 61% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, H, J, O, Q, V, X | Tubulin alpha-1A chain | protein | 423 | 45% helix, 17% strand | P02550 |
| B, D, I, K, P, R, W, Y | Tubulin beta chain | protein | 424 | 47% helix, 17% strand | P02554 |
| E | Protein STU2P/ALP14P | protein | 491 | 67% helix, 0% strand | — |
| F, G, M, N, T, U, a, b | Designed ankyrin repeat protein (darpin) D1 | protein | 155 | 56% helix, 0% strand | — |
| L | Protein STU2P/ALP14P | protein | 494 | 68% helix, 0% strand | — |
| S | Protein STU2P/ALP14P | protein | 493 | 68% helix, 0% strand | — |
| Z | Protein STU2P/ALP14P | protein | 495 | 68% helix, 0% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 8 copies · chains A, B, C, D, H, I, J, K, O, P, Q, R, V, W, X, Y
- GDP · Guanosine-5'-diphosphate · ligand · 8 copies · chains B, D, I, K, P, R, W, Y
- MG · Magnesium ion · metal · 16 copies · chains A, B, C, D, H, I, J, K, O, P, Q, R, V, W, X, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 781 | 0.81 | 0.85 | 88 | empty |
| 2 | 965 | 0.80 | 0.82 | 95 | GTP, MG |
| 3 | 986 | 0.80 | 0.81 | 98 | GTP, MG |
| 4 | 982 | 0.80 | 0.81 | 91 | GTP, MG |
| 5 | 428 | 0.79 | 0.88 | 56 | GTP, MG |
Interfaces
46 interfaces between chains.
- H–I · 1412 Ų buried · 16 hydrogen bonds · protein-protein
- V–W · 1405 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1397 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1371 Ų buried · 13 hydrogen bonds · protein-protein
- Q–R · 1359 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6MZF · Structural Basis of Tubulin Recruitment and Assembly by Microtubule Polymerases with… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P02550
- Every structure of UniProt P02554
- Elsewhere: RCSB PDB 6MZF · PDBe 6MZF · UniProt P02550 · UniProt P02554
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